Genome-wide identification of vegetative phase transition-associated microRNAs and target predictions using degradome sequencing in Malus hupehensis

Abstract

BackgroundA long juvenile period between germination and flowering is a common characteristic among fruit trees, including Malus hupehensis (Pamp.) Rehd., which is an apple rootstock widely used in China. microRNAs (miRNAs) play an important role in the regulation of phase transition and reproductive growth processes.ResultsM. hupehensis RNA libraries, one adult and one juvenile phase, were constructed using tree leaves and underwent high-throughput sequencing. We identified 42 known miRNA families and 172 novel miRNAs. We also identified 127 targets for 25 known miRNA families and 168 targets for 35 unique novel miRNAs using degradome sequencing. The identified miRNA targets were categorized into 58 biological processes, and the 123 targets of known miRNAs were associated with phase transition processes. The KEGG analysis revealed that these targets were involved in starch and sucrose metabolism, and plant hormone signal transduction. Expression profiling of miRNAs and their targets indicated multiple regulatory functions in the phase transition. The higher expression level of mdm-miR156 and lower expression level of mdm-miR172 in the juvenile phase leaves implied that these two small miRNAs regulated the phase transition. mdm-miR160 and miRNA393, which regulate genes involved in auxin signal transduction, could also be involved in controlling this process. The identification of known and novel miRNAs and their targets provides new information on this regulatory process in M. hupehensis, which will contribute to the understanding of miRNA functions during growth, phase transition and reproduction in woody fruit trees.ConclusionsThe combination of sRNA and degradome sequencing can be used to better illustrate the profiling of hormone-regulated miRNAs and miRNA targets involving complex regulatory networks, which will contribute to the understanding of miRNA functions during growth, phase transition and reproductive growth in perennial woody fruit trees.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1125) contains supplementary material, which is available to authorized users.

Shoot bending promotes flower bud formation by miRNA‐mediated regulation in apple (Malus domestica Borkh.)

“…For the six miRNA libraries, the reads’ size distributions were quite similar (Figure S4), but the read size distribution in the degradome library was significantly different from those of the miRNA libraries (Figure S2). The length of sRNA varied, with 21‐, 22‐, 23‐ and 24‐nt small RNAs forming the major population, and 24 nt was the most dominant length in the six libraries (Figure S1), which was similar to the results obtained from other plants, such as Malus hupehensis and Arabidopsis thaliana (Confraria et al ., ; Xing et al ., ). The total raw reads were categorized into 12 different classes, exon _antisense (0.91%), exon_sense (1.42%), intron _antisense (2.31%), intron_sense (2.72%), miRNA (2.50%), rRNA (19.16%), repeat (3.04%), scRNA (0), snRNA (0.02%), snoRNA (0.02%), tRNA (2.06%) and others (65.83%), for the CES library (Table S3), by matching them to the domesticated apple's genome in the Rfam (http://www.sanger.ac.uk/resources/databases/rfam.html) and GenBank (http://www.ncbi.nlm.nih.gov/genbank) databases using the tag2annotation software.…”

“…Similar results can be seen in Xing et al . (). In addition, the expression levels of these identified known miRNAs in the six libraries between shoot‐bending and control treatments were divided into eight different categories based on their read content's frequencies, with almost no differences among the libraries (Figure ).…”

“…The methods of small RNAs extraction and enrichment can be seen in Xing et al . (). First, total RNA extractions from six buds libraries were performed using the RNeasyPlant Mini Kit (Qiagen, Hilden, Germany), and each was collected into RNA pools for small RNA construction.…”

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

“…Thus, if there are mRNAs cleaved by a miRNA after its 10 th nucleotide, one would observe alignment of RNA termini matching the predicted miRNA binding site. Degradome analysis usually defines a category of transcripts predicted to be endonucleolytically cleaved and then are cleavage positions compared to predicted miRNA binding sites (Li and Sunkar, 2013;Xing et al, 2014;Ding et al, 2016;Fan et al, 2016;Wang et al, 2016). Degradome analysis and target prediction has been integrated in to a web resource comPARE for plant miRNA target analysis (Kakrana et al, 2014).…”

Effects of CEPA and 1-MCP on flower bud differentiation of apple cv. ‘Nagafu No.2’ grafted on different rootstocks

“…Researchers have done a lot of research on the regulation of GA on flower bud 4 0 9 differentiation in fruit trees (Xing et al, 2014;Yamaguchi et al, 2014). Apart from significant difference after spraying with 1-MCP (Table 1).…”